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Potassium in PDB 6rjr: Crystal Structure of A Fungal Catalase at 1.9 Angstrom

Enzymatic activity of Crystal Structure of A Fungal Catalase at 1.9 Angstrom

All present enzymatic activity of Crystal Structure of A Fungal Catalase at 1.9 Angstrom:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure of A Fungal Catalase at 1.9 Angstrom, PDB code: 6rjr was solved by S.Gomez, S.Navas-Yuste, A.M.Payne, W.Rivera, M.Lopez-Estepa, C.Brangbour, D.Fulla, J.Juanhuix, F.J.Fernandez, M.C.Vega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.98 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.670, 131.620, 176.670, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24.1

Other elements in 6rjr:

The structure of Crystal Structure of A Fungal Catalase at 1.9 Angstrom also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom (pdb code 6rjr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom, PDB code: 6rjr:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6rjr

Go back to Potassium Binding Sites List in 6rjr
Potassium binding site 1 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K609

b:48.2
occ:1.00
 O A:HOH892 2.4 24.3 1.0
O A:GLY208 2.5 13.7 1.0
O A:LYS292 2.6 31.0 1.0
O A:PRO140 2.6 14.2 1.0
O A:HOH819 2.8 27.1 1.0
C A:GLY208 3.6 17.8 1.0
C A:LYS292 3.7 24.8 1.0
C A:PRO140 3.8 22.4 1.0
NE2 A:GLN224 3.8 21.4 1.0
OE1 A:GLN224 3.9 23.9 1.0
O A:LEU290 3.9 16.1 1.0
CA A:GLY208 4.1 13.4 1.0
CG1 A:VAL141 4.2 21.6 1.0
CD A:GLN224 4.2 21.0 1.0
CA A:VAL293 4.3 22.8 1.0
N A:VAL293 4.4 13.9 1.0
C A:LEU290 4.5 20.7 1.0
CA A:VAL141 4.5 22.0 1.0
N A:LYS292 4.6 24.3 1.0
CG1 A:VAL293 4.6 17.1 1.0
N A:VAL141 4.6 19.3 1.0
CA A:PRO140 4.7 17.4 1.0
CB A:PRO140 4.7 27.1 1.0
O A:ASP289 4.8 17.5 1.0
N A:HIS209 4.8 15.9 1.0
CA A:LYS292 4.8 20.6 1.0
CA A:LEU290 4.8 19.9 1.0
O A:HOH926 4.9 18.9 1.0
CD1 A:LEU290 4.9 22.8 1.0
O A:HOH835 5.0 31.8 1.0

Potassium binding site 2 out of 4 in 6rjr

Go back to Potassium Binding Sites List in 6rjr
Potassium binding site 2 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:72.3
occ:1.00
 O B:PRO140 2.5 32.6 1.0
O B:LYS292 2.6 45.6 1.0
O B:HOH804 2.6 44.8 1.0
O B:GLY208 2.7 31.5 1.0
O B:HOH859 2.8 36.6 1.0
C B:LYS292 3.7 46.8 1.0
C B:PRO140 3.7 31.4 1.0
C B:GLY208 3.7 44.7 1.0
O B:LEU290 3.8 34.5 1.0
NE2 B:GLN224 4.1 39.0 1.0
CA B:GLY208 4.1 31.3 1.0
CG1 B:VAL141 4.1 32.6 1.0
OE1 B:GLN224 4.2 44.3 1.0
CA B:VAL293 4.2 37.5 1.0
N B:VAL293 4.3 46.1 1.0
CD B:GLN224 4.4 40.0 1.0
CA B:VAL141 4.5 31.5 1.0
C B:LEU290 4.6 36.1 1.0
CA B:PRO140 4.6 40.9 1.0
N B:VAL141 4.6 32.4 1.0
CB B:PRO140 4.6 36.8 1.0
N B:LYS292 4.6 35.0 1.0
O B:ASP289 4.7 29.1 1.0
CA B:LYS292 4.8 42.9 1.0
CB B:VAL293 4.8 42.5 1.0
CG2 B:VAL293 4.9 46.6 1.0
N B:HIS209 4.9 29.4 1.0
CA B:LEU290 4.9 32.4 1.0
CD1 B:LEU290 4.9 32.6 1.0
CB B:VAL141 5.0 31.5 1.0

Potassium binding site 3 out of 4 in 6rjr

Go back to Potassium Binding Sites List in 6rjr
Potassium binding site 3 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K605

b:47.0
occ:1.00
 O C:GLY208 2.5 16.3 1.0
O C:LYS292 2.6 33.6 1.0
O C:HOH785 2.6 17.0 1.0
O C:HOH875 2.7 27.7 1.0
O C:PRO140 2.7 21.1 1.0
C C:GLY208 3.5 15.9 1.0
O C:LEU290 3.7 28.4 1.0
NE2 C:GLN224 3.7 27.2 1.0
C C:LYS292 3.8 20.5 1.0
C C:PRO140 3.9 15.5 1.0
CA C:GLY208 4.1 20.3 1.0
OE1 C:GLN224 4.2 35.3 1.0
C C:LEU290 4.3 19.4 1.0
CG1 C:VAL141 4.3 22.9 1.0
CD C:GLN224 4.3 32.4 1.0
O C:ASP289 4.4 24.5 1.0
CA C:VAL293 4.5 20.0 1.0
CA C:LEU290 4.5 17.4 1.0
CD1 C:LEU290 4.5 19.8 1.0
N C:VAL293 4.6 22.2 1.0
N C:LYS292 4.6 19.2 1.0
CA C:VAL141 4.6 18.8 1.0
O C:HOH914 4.6 19.8 1.0
N C:HIS209 4.7 26.0 1.0
O C:HOH878 4.7 24.0 1.0
N C:VAL141 4.7 19.5 1.0
O C:HOH724 4.7 44.0 1.0
CG1 C:VAL293 4.8 16.9 1.0
CA C:LYS292 4.8 21.9 1.0
CA C:PRO140 4.9 43.9 1.0
CB C:PRO140 5.0 27.7 1.0
CA C:HIS209 5.0 22.9 1.0

Potassium binding site 4 out of 4 in 6rjr

Go back to Potassium Binding Sites List in 6rjr
Potassium binding site 4 out of 4 in the Crystal Structure of A Fungal Catalase at 1.9 Angstrom


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of A Fungal Catalase at 1.9 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K606

b:53.0
occ:1.00
 O D:PRO140 2.5 24.4 1.0
O D:GLY208 2.5 19.3 1.0
O D:LYS292 2.6 28.7 1.0
O D:HOH889 2.8 16.0 1.0
O D:HOH876 2.8 41.3 1.0
C D:GLY208 3.5 31.9 1.0
O D:LEU290 3.6 22.2 1.0
C D:PRO140 3.7 18.1 1.0
C D:LYS292 3.8 16.6 1.0
CG1 D:VAL141 3.8 15.4 1.0
CA D:GLY208 3.9 12.5 1.0
NE2 D:GLN224 4.2 30.5 1.0
C D:LEU290 4.2 15.2 1.0
CA D:VAL141 4.3 16.4 1.0
OE1 D:GLN224 4.3 24.6 1.0
CA D:VAL293 4.4 17.6 1.0
N D:VAL141 4.5 20.4 1.0
N D:VAL293 4.5 24.4 1.0
CA D:LEU290 4.5 20.5 1.0
N D:LYS292 4.5 24.2 1.0
CD1 D:LEU290 4.6 18.8 1.0
O D:ASP289 4.6 24.8 1.0
CD D:GLN224 4.6 33.3 1.0
CG1 D:VAL293 4.6 32.3 1.0
CA D:PRO140 4.7 24.4 1.0
N D:HIS209 4.7 21.4 1.0
CB D:VAL141 4.7 28.1 1.0
CB D:PRO140 4.8 16.2 1.0
CA D:LYS292 4.8 18.6 1.0
O D:HOH943 4.9 41.6 1.0
N D:GLY208 5.0 27.8 1.0

Reference:

S.Gomez, S.Navas-Yuste, A.M.Payne, W.Rivera, M.Lopez-Estepa, C.Brangbour, D.Fulla, J.Juanhuix, F.J.Fernandez, M.C.Vega. Peroxisomal Catalases From the Yeasts Pichia Pastoris and Kluyveromyces Lactis As Models For Oxidative Damage in Higher Eukaryotes. Free Radic. Biol. Med. V. 141 279 2019.
ISSN: ISSN 1873-4596
PubMed: 31238127
DOI: 10.1016/J.FREERADBIOMED.2019.06.025
Page generated: Mon Aug 12 17:28:25 2024

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